How Electron Microscopes Pioneered Atom Microscopy

The history and growth of microscopy may have started by accident or through simple curiosity, but much like everything else in modern civilization, it has evolved largely to accommodate a certain need, which, at its core, is to look at the smallest possible thing as magnified as possible.

And for science, that means being able to see right down to every single atom. The question is, what type of microscope can do just that?

What microscope can see atoms?

The introduction of a new type of microscope, called the electron microscope, has enabled scientists and researchers to image various materials at an unprecedented level of magnification and resolution that has never been done before.

These microscopes have the capability to image almost any material, from razor thin layers to particles that are millions of times thinner than a single strand of hair. And, these can reveal various properties of the material, right down to the atomic level, giving us actual images of single atoms and atomic columns.

Electron microscopes have a multitude of uses. Here is where and how electron microscopes can be used, as well as the different types of electron microscopes.

Atoms that you can see using electron microscope

What is the purpose of an electron microscope?

This unique ability of electron microscopes allows us to see exactly what is in any given material, down to the details of each atom, something that, for many years, has always been just a concept, and nothing more.

Being able to see the atomic makeup of a material reveals important information not only on the properties of this material but more importantly, the underlying mechanisms behind these properties. 

By being able to see why and how atoms group together in a certain way, we can understand how each atom contributes to any given property of that material, such as its strength and conduciveness. We’ll also know whether the material is exhibiting any unusual properties.


What can you do with an electron microscope?

With such a powerful imaging device, the possibilities are limitless. Some electron microscopes have exhibited the ability to image certain materials that are typically transparent to electrons, especially elements whose atoms are lightweight. 

We can also track and map the magnetic and electric fields within the material by measuring the electrons’ phase. And, even rendering a three-dimensional model is possible by using multiple photographs of the material taken at different angles.

With all this information, we can now make use of and manipulate these materials in a way that was not possible before.

What materials can be imaged with an electron microscope?

An image of an ant in a scanning electron microscope

The beauty of electron microscopes is that these are versatile and all-around imaging devices that can be used for just about any type of material, whether it be organic or inorganic, live or fixed, and so on.

Some of the many different kinds of specimens observed under an electron microscope include microorganisms such as tiny animals and parasites, certain parts of plants, a variety of cells and individual parts of these cells, pathogens and viruses, chemical compounds and chemical reactions, and even crystals, metals, and dust particles from outer space.

What are the applications of electron microscopy?

The ability to look at any material’s atomic makeup opens a door of opportunity not only in modifying this material, but in creating a brand new material altogether. This is because rearranging and manipulating even a single atom of a material can drastically change its properties and affect its catalysis.

This is why for every decade that electron microscopes have been operated, leaps of advancements have happened in many different disciplines, including biology, life sciences, materials research, semiconductors, data storage, chemistry, food science, mining, pharmacology, forensics, and nanotechnology, including nanomedicine.

What is nanotechnology?

Nanotechnology is essentially the study and application of how matter works and can be manipulated in the atomic, molecular, and supramolecular scale. This is generally pursued the purposes of manufacturing advanced technological products for industrial and mass consumption.

The main reason that this is possible is because of electron or atom microscopy, enabling research and development industries to see, understand, and manipulate particles of matter that are smaller than a single nanometer.

How does an electron microscope work?

The basic facet of electron microscopy is utilizing beams of supercharged electrons to produce a highly magnified image of a specimen. Electron microscopes have the capacity to magnify things for more than 500,000 times, and this is coupled with an extreme resolution that shows clear details of up to a single nanometer or less.

This high magnification and resolution are what enables us to see plenty of details inside the material, down to each nanoparticle and atom. The rendered images typically appear in grayscale and are then colorized afterwards through various imaging software.

How the microscope works exactly depends on which type of electron microscope we are talking about.

Electron microscope vs compound microscope

The main difference between electron microscopes and compound light microscopes is how the magnified image is produced, which is largely based on their “light” source. A compound light microscope uses typical visible light, which has a relatively long wavelength, whereas electron microscopes use a beam of electrons.

As such, compound microscopes only have a maximum of 2000x magnification power, and a resolving power that allows us to see details of objects more than 300 nanometers in size. This is plenty enough to look at plant and animal cells, but not much further, since the light misses tinier details and therefore cannot reflect them without being distorted, or at all.

On the other hand, the beam of electrons used in electron microscopes has a wavelength that is thousands of times shorter than that of visible light, making it fundamentally better than visible light when it comes to magnification and resolution capabilities.

What are the types of electron microscopes?

Types of electron microscopes

There are actually three different types of electron microscopes- the scanning electron microscope, transmission electron microscope, and scanning transmission electron microscope. 

Each of these microscopes has slightly different functions and operating techniques. But, they all have magnetic fields that generate an electron optical lens system which has the capacity to focus electrons, as well as an ultra-sensitive camera and a frame grabber that can register individual electrons.


Scanning electron microscope (SEM)

A scanning electron microscope works by shining down a beam of electrons on a rectangular area of the specimen, which, once hit, reflects and scatters high energy electrons, and emits low energy secondary electrons. 

These are then scanned by a detector that generates an image of that specimen, along with other forms of energy loss from the specimen, including the emission of heat, light, and X-rays, all of which offer valuable information about the specimen.

These are excellent for viewing the surfaces of minute three-dimensional specimens, or even specific regions of the specimen, including insects and parasites such as lice, mites, and flies. Although usually, the specimen may need to be coated, stained, or chemically treated.

Cryo scanning electron microscope

A specialized form of scanning electron microscopy is the cryo-SEM, which is used for viewing materials that contain moisture, such as plants, food, and even snowflakes. 

With this technique, the specimen is frozen in liquid nitrogen prior to viewing, in order to preserve the structural integrity of the specimen. This makes for an accurate representation of the specimen.

Electron backscatter diffraction

Not an entire electron microscope per se, but an additional imaging tool used with a scanning electron microscope, an electron backscatter diffraction (EBSD) detector is used to study minerals in detail, including its structure and crystallization.

Transmission electron microscope (TEM)Transmission electron microscope

On the other hand, a transmission electron microscope is excellent for studying the structure of smaller specimens such as blood cells. It works more similarly to a compound light microscope that shines light through the specimen, only here, what’s transmitted through the specimen is a beam of electrons.

This high voltage electron beam comes from an electron gun with a tungsten filament cathode. It’s accelerated by an anode, and is focused by electrostatic and electromagnetic lenses, all before passing through the specimen.

This beam is then received by a fluorescent screen, which is where the specimen image is formed, much like how a projector screen works. TEMs are used for specimens with a maximum thickness of 100 nanometers, and are able to show detailed atoms and nanoparticles.

Electron tomography

A specialized form of transmission electron microscopy is electron tomography, which is used when a higher resolution of a two-dimensional image of the specimen is needed. 

More importantly, however, it’s used for rendering three-dimensional images of the specimen, which better showcases the specimen’s properties and how each of its structural components relate to each other.

Reflection electron microscope

A slightly different version of the transmission electron microscope is the reflection electron microscope (REM). It also works by transmitting a beam of electrons to the specimen, but the key difference is that the resulting image is formed using a reflected beam of elastically scattered electrons.

It has a couple of other variations such one that is specialized for viewing microstructures of magnetic domains, and it’s usually used with complementary techniques such as reflection high-energy loss spectroscopy and reflection high energy electron diffraction.

Serial section electron microscopy

Another application of transmission electron microscopy is with serial section electron microscopy (sSEM), which is used to study a variety of organic materials, such as when imaging sequential sections of brain tissue, and analyzing its connectivity through volumetric samples.

Scanning transmission electron microscope (STEM)

And then there is the scanning transmission electron microscope, which combines the best features and capabilities of SEMs and TEMs. This microscope can transmit an image of the entire specimen, and simultaneously scan a certain region of that specimen.

It makes use of a focus incident probe that is run across the specimen in order to detect scattered electrons throughout the specimen. It’s a high-resolution microscope that has the ability to get rid of specimen and image aberrations.

STEMs are rapidly becoming popular and sought after, since these microscopes are useful imaging devices that are compatible with a variety of tools and techniques that can further analyze the specimen and its nature. These include spectroscopy techniques such as those that use energy dispersive X-rays and electron energy loss.

The development of electron microscopes

Atom microscopy, or the use of microscopes to see atoms, began with the creation of the first electron microscope, which was, in a way, a lot similar to a modern light microscope. And, it actually wasn’t until the mid 1900’s that the first electron microscope was invented.

The first electron microscope

The first electron microscope
Electron microscope constructed by Ernst Ruska in 1933

The first ever electron microscope was invented in 1931 by physicist Ernst Ruska and electrical engineer Max Knoll. This microscope was reportedly capable of a four hundred power magnification, and was the first ever microscope that was able to demonstrate the principles of electron and atom microscopy.

While these two individuals are largely credited for the invention of the electron microscope, however, several other names come into light when talking about the development of the electron microscope.

Some of them are Hans Busch who developed the electromagnetic lens in 1926, Leó Szilárd and Dennis Gabor who applied for a patent for an electron microscope in 1928, and Reinhold Rudenberg who successfully obtained a patent in 1931.

Developments on the first design

In the following years, many more individuals, including Ernst Ruska, further developed the electron microscope, first by increasing its resolution to more than that of any light microscope, then by developing specialized applications for biological specimens.

The conception of the scanning electron microscope followed suit in 1937, then the transmission electron microscope in 1939, both based on the prototype by Ernst Ruska.

Other microscopes that can see atoms and beyond

Apart from these high powered electron microscopes that enable us to look at materials down to the atomic level, there are many other microscopes and imaging devices that have recently been developed to the same, and better.

Scanning probe microscope

While electron microscopes gave us the ability to see individual atoms, it’s not quite enough for us to glimpse its intricate details. What gives us this power is the scanning probe microscope, which uses neither light nor electrons.

It has a nanoscale “finger” that probes the surface of the specimen to give us a better idea of its properties. Thus, this microscope is what gives us the ability to manipulate and move around individual atoms.

There are, in fact, three types of scanning probe microscopes:

  • Atomic force microscope– this features a fine tip that’s only a few atoms wide and has the capability to produce three-dimensional images of atoms.
  • Scanning tunneling microscope– this also has a probing tip, but it works by measuring the electric current between the specimen’s atoms and the probe tip.
  • Magnetic force microscope– the tip of this microscope is used to track and monitor any change in the specimen atoms’ magnetic structure.

What are the disadvantages of electron microscopes?

It’s certainly true that electron microscopes have pioneered atom microscopy, which has propelled science and technology into a new era. But, electron microscopes do not come without their fair share of disadvantages.

Cost of production

One very limiting issue is that these microscopes are expensive to manufacture and maintain, with costs of production and upkeep running millions of dollars. 

This is mainly why there are few electron microscopes out there, added to the fact that they need to be housed in a special, often underground, facility equipped with magnetic field canceling systems.

Viewing environment

Another important thing is that for most electron microscopes, the specimen needs to be placed in a vacuum chamber in order to prevent air molecules and particles from disrupting the path of the electrons to and from the specimen.

This means that specimens need to be prepared beforehand through a variety of procedures including dehydration. Moreover, liquid and gaseous specimens require specialized electron microscopes and techniques such as liquid-phase electron microscopy, environmental scanning electron microscopy, and in-situ electron microscopy.

Specimen preparation

More on specimen sample preparation, these procedures are often costly and labor intensive, and many of these procedures somewhat alter the appearance and structural integrity of the specimen.

Common sample preparation techniques include the application of a conductive coating, pressurization, stabilization, ultra-thin sectioning, staining, cryofixation, vitrification, chemical fixation, embedding, sectioning, metal shadowing, and earthing.



The unprecedented ability to see individual atoms of any object or material, a.k.a atom microscopy, is made possible with the invention of electron microscopes. These are special types of microscopes that make use of electron beams to render high contrast images of the specimen, which offers clear and intricate details down to the atomic level.

As such, electron microscopes have become extremely valuable imaging devices across many different fields of study and research, and have immensely helped in the production of newer and more technologically advanced products for our consumption, including mobile devices.

Microscopy has for many centuries catered to mankind’s need for evolution and development, and atom microscopy is just one of the many latest technologies available for us.

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